Summary: Flagellar motor switch protein FliM

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Wikipedia: Flagellar motor switch
Pfam
InterPro

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Flagellar motor switch

FliG C-terminal domain

crystal structure of the middle and c-terminal domains of the flagellar rotor protein flig

Identifiers

Symbol

FliG_C

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Flagellar motor switch protein FliM

Identifiers

Symbol

FliM

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

In molecular biology, the flagellar motor switch is a protein complex. In Escherichia coli and Salmonella typhimurium it regulates the direction of flagellar rotation and hence controls swimming behaviour.^[1] The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour.^[1] CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated.

The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN.^[2] Several amino acids within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important.^[2] Such clustering suggests that FliG-FliM interaction plays a central role in switching.

Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins.^[3] This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring.^[3]^[4] FliG is present in about 25 copies per flagellum. The structure of the C-terminal domain of FliG is known, this domain functions specifically in motor rotation.^[5]

[edit] References

^ ^a ^b Roman SJ, Frantz BB, Matsumura P (October 1993). "Gene sequence, overproduction, purification and determination of the wild-type level of the Escherichia coli flagellar switch protein FliG". Gene 133 (1): 103–8. doi:10.1016/0378-1119(93)90232-R. PMID 8224881.
^ ^a ^b Marykwas DL, Berg HC (March 1996). "A mutational analysis of the interaction between FliG and FliM, two components of the flagellar motor of Escherichia coli". J. Bacteriol. 178 (5): 1289–94. PMC 177801. PMID 8631704. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=177801.
^ ^a ^b Kihara M, Homma M, Kutsukake K, Macnab RM (June 1989). "Flagellar switch of Salmonella typhimurium: gene sequences and deduced protein sequences". J. Bacteriol. 171 (6): 3247–57. PMC 210043. PMID 2656645. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=210043.
^ Francis NR, Irikura VM, Yamaguchi S, DeRosier DJ, Macnab RM (July 1992). "Localization of the Salmonella typhimurium flagellar switch protein FliG to the cytoplasmic M-ring face of the basal body". Proc. Natl. Acad. Sci. U.S.A. 89 (14): 6304–8. doi:10.1073/pnas.89.14.6304. PMC 49489. PMID 1631122. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=49489.
^ Lloyd SA, Whitby FG, Blair DF, Hill CP (July 1999). "Structure of the C-terminal domain of FliG, a component of the rotor in the bacterial flagellar motor". Nature 400 (6743): 472–5. doi:10.1038/22794. PMID 10440379.

This article incorporates text from the public domain Pfam and InterPro IPR001689

This article incorporates text from the public domain Pfam and InterPro IPR000090

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Flagellar motor switch protein FliM

No Pfam abstract.

Clan

This family is a member of clan CheC-like (CL0355), which has a total of 4 members.

External database links

PANDIT:	PF02154
PRINTS:	PR00955
Pseudofam:	PF02154
SYSTERS:	FliM

This tab holds annotation information from the InterPro database.

InterPro entry IPR001689

The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour [PUBMED:8224881]. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour [PUBMED:8224881]. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated.

The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN [PUBMED:8631704]. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N or C termini being less important [PUBMED:8631704]. Such clustering suggests that FliG-FliM interaction plays a central role in switching.

Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins [PUBMED:2656645]. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [PUBMED:2656645, PUBMED:1631122].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Cellular component	bacterial-type flagellum basal body (GO:0009425)
Molecular function	motor activity (GO:0003774)
Biological process	ciliary or flagellar motility (GO:0001539)
Biological process	chemotaxis (GO:0006935)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan CheC-like (CL0355), which contains the following 4 members:

CheC CheX DUF3334 FliM

Alignments

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

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Alignment:	Seed (7) Full (1304) NCBI (1123) Metagenomics (440)
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Alignment:	Seed (7) Full (1304)
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Sequence:	Inserts lower case All upper case
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Download/view:	Download View

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Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (7) Full (1304) NCBI (1123) Metagenomics (440)
Full length sequences	Full-sequences (1304)

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed or full alignments.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

IPR001689

Previous IDs:

none

Type:

Family

Author:

Mian N, Bateman A

Number in seed:

7

Number in full:

1304

Average length of the domain:

191.30 aa

Average identity of full alignment:

36 %

Average coverage of the sequence by the domain:

57.06 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.4	20.4
Trusted cut-off	20.4	20.5
Noise cut-off	20.3	20.3

Model length:

192

Family (HMM) version:

10

Download:

download the raw HMM for this family

Species distribution

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Colour assignments

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab if you need to select sub-trees and view sequence alignments. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

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The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, it's distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Family: FliM (PF02154)

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Summary: Flagellar motor switch protein FliM

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Flagellar motor switch

[edit] References

Flagellar motor switch protein FliM

Clan

External database links

InterPro entry IPR001689

Gene Ontology

Domain organisation

Pfam Clan

Alignments

Viewing

Downloading

View options

Formatting options

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree